yes, if you use the 'uninstall' file from the flashme site, that should put everything back to normal condition, I would think (I haven't done it personally, though, so you can wait for someone else to post for verification purposes).
Flashme is more fail-safe than the original firmware because of it's bios recovery feature. Only part of the firmware is protected, so dangerous programs like ds bricker can ruin your original firmware.
But you mentioned you're not using homebrew anymore, so you will probably be ok anyways.
BruceG